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The archaeogenomics of domestic animals (CANCELLED)

From 11 May 2020 until 15 May 2020 - CIBIO-InBIO, Vairão, Portugal
The archaeogenomics of domestic animals (CANCELLED)

It is now generally agreed that diachronic genetic studies are required in order to infer the origins and evolutionary trajectories of domestic animals. Data spanning long time scales from zooarchaeological specimens allow the investigation of genetic variation within populations over time. Analysis of ancient DNA opens a direct window into the past for reconstruction of the genetic history of animal populations.

The objective of this course is to provide an overview of the most recent Archaeogenomics findings on the origin and evolution of domestic animals. It will also cover some of the recommended bioinformatics tools and methods for the study of ancient DNA genomics data. There will be hands-on sessions, including bioinformatics on how to filter, infer damage patterns and authenticate next-generation-sequencing data obtained from archaeological specimens, as well as on population genomics. One invited speaker in Archaeogenomics will also contribute to the course.

At the end of the course students should understand the importance of including genomic data concerning past populations to make evolutionary inferences, as well as get familiar with the challenges and peculiarities of ancient DNA analysis.

Topics that will be discussed:
- Animal evolution and population dynamics
- Phylochronological studies
- Domestication events
- Livestock improvement
- Zooarchaeology: radiocarbon dating, isotope analysis and osteometry
- Population Genomics

- Ancient DNA data analysis



May 11

10:00-10:30 – Course Introduction
10:30-11:30 – Zooarchaeology of domestic animals | S Davis
12:00-13:00 – Hands-on Zooarchaeology | S Davis
14:00-16:00 – Hands-on Zooarchaeology | S Davis
16:30-17:30 – The origin and subsequent evolution of the dog | AE Pires
17:30-18:00 – Art & Science: Digital animation – "The Muge dog – a pre-historic friend” | AE Pires

May 12

09:30-11:30 – Recap (30 min). Archaeobotany of domesticated plants | J Tereso
12:00-13:00 - Hands-on Archaeobotany | J Tereso
14:00-16:00 – Genomic studies on aurochs and their domestic counterparts | C Ginja
16:30-18:00 – Hands-on Geoarchaeology | A Costa, S Gabriel, AE Pires

May 13

09:30-11:30 - Recap (30 min). Demography and Approximate Bayesian Simulation | L Chikhi
12:00-13:00 - Hands-on Population demography | L Chikhi
14:00-16:00 - Hands-on Population demography | L Chikhi
Coffee break
16:30-18:00 - Hands-on Population demography | L Chikhi

May 14

09:30-11:30 - Recap (30 min). Low-cost high-throughput metabarcoding for degraded samples | S Guimarães
12:00-13:00 - Hands-on Archaeogenomics data analysis | C Ottoni
14:00-16:00 - Hands-on Archaeogenomics data analysis | C Ottoni
16:30-18:00 - Hands-on Archaeogenomics data analysis | C Ottoni

May 15

09:30-11:30 - Recap (30 min). Hands-on Archaeogenomics data analysis | C Ottoni
12:00-13:00 - Concluding session and evaluation. General conclusions.
15:30-16:30 - Senior seminar in Biodiversity & Evolution (open to the scientific community) - Oral microbiomes from the past: reconstructing health, diet and lifestyles through dental calculus analysis - C Ottoni



Catarina Ginja - CIBIO-InBIO | ARCHGEN
Sílvia Guimarães - CIBIO-InBIO | ARCHGEN
Ana Elisabete Pires - LARC-DGPC and CIBIO-InBIO | ARCHGEN
Sónia Gabriel - LARC-DGPC
Ana Costa - LARC-DGPC
Claudio Ottoni - University of Rome
Lounés Chikhi - Instituto Gulbenkian de Ciência


The course will be open to a maximum number of 20 participants.


75% of available student slots are reserved for BIODIV students.
Priority will be given to:
• 1st year and other PhD students attending the BIODIV Doctoral Program;
• PhD students attending other courses;
• Other post-graduate students and researchers.



Participants are advised to bring their own laptop
All sessions will be in English.


Participation is free of charge for BIODIV students | 95 € (students) | 200 € (other participants). CIBIO-InBIO members will have an additional discount of 20%.


Registration deadline: March 13, 2020
All applicants will be notified whether they are accept by March 18, 2020


Please note that new rules apply for all BIODIV students.




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